Accumulating evidence revealed that some probiotics regulated lipid metabolism and alleviated diet-induced non-alcoholic fatty liver disease (NAFLD). This study mainly explored whether yogurt-derived Lactobacillus plantarum Q16 modulated lipid and energy metabolism, and suppressed microbial dysbiosis in high-fat diet (HFD)-fed mice. Results showed that oral administration of L. plantarum Q16 improved serum and hepatic lipid profi le. Protein analysis showed that L. plantarum Q16 could reduce hepatic lipid content by reducing the expression of FAS, ACC, SCD-1, Srebp-1c and ATGL, but increasing expression levels of CPT-1α, PPAR-α and ATGL. Meanwhile, L. plantarum Q16 also improved hepatic energy metabolism by regulating FGF21/adiponectin/AMPKα/PGC-1α signaling pathway. Metagenomic analysis also discovered that L. plantarum Q16 increased species diversity and richness of intestinal microbiota, promoted proliferation of benefi cial commensals and suppressed the growth of endotoxin-producing microorganisms in the colon of HFD-fed mice. Overall, L. plantarum Q16 protected against HFD-induced NAFLD by improving hepatic profi le and regulating colonic microbiota composition.